Genome‑wide analysis of the CaWRKY transcription factors reveals CaWRKY28 as a candidate gene for cold tolerance breeding in Coffea arabica L.

BACKGROUND: In China, over 98% of coffee is produced in Yunnan Province, where Coffea arabica L. predominates. Cold stress represents a major genetic constraint limiting coffee production, especially during the fruiting stage. WRKY transcription factors (TFs) are key regulators of stress responses, yet their systematic characterization and breeding value in C. arabica L. are remain largely unexplored. RESULTS: Here, we conducted a genome-wide analysis of WRKY genes across four C. arabica L. genomes, identifying 400 CaWRKY members phylogenetically classified into three groups. Segmental duplication was identified as the primary driver for CaWRKY family expansion. Physiological assessment of fruiting trees under cold stress revealed significant alterations in key traits, including increased electrolyte leakage and soluble sugars, and decreased photosynthesis. Transcriptomic analysis identified 47 cold-responsive CaWRKYs, which can be classified into five clusters, with CaWRKY28, 82, 85, 86, and 89 showing up‑regulation under cold treatment. Crucially, heterologous expression of CaWRKY28 in yeast conferred significantly enhanced cold tolerance, functionally validating its role in stress adaptation. CONCLUSIONS: Our study provides the first comprehensive genetic overview of the CaWRKY family in C. arabica L. and pinpoints CaWRKY28 as a high-value candidate for molecular breeding aimed at enhancing cold tolerance in this vital crop.